Files in yujijun/neoantigenML
Machine Learning Methods for Neoantigen Filtering
.Rbuildignore
.gitignore
DESCRIPTION
NAMESPACE
NeoantigenML.Rproj
R/FeatureCorrelation.R
R/HyperparameterTuning.R
R/Interpretation.R
R/PepDataVis.R
R/PepFeatureSelect.R
R/PerformanceEva.R
R/PropertyofPepInterPotential.R
R/PropertyofPepMutaion.R
R/PropertyofPepSingle.R
R/README.md
R/base.r
R/data.R
R/dataset.r
R/installpak_Repitope.R
R/neoantigenML.R
R/pepClustering.R
R/pepKmerFeature.R
R/pepMotif.R
R/pepVisualization.R
README.md
data-raw/final.neg.neoantigens.filtered.tsv
data-raw/final.pos.neoantigens.filtered.tsv
data-raw/output.property.csv
data/MLtestData.rda
data/Neodataset.rda
data/T.rda
data/alltestML.rda
data/deredundancy.allclean.rda
data/deredundancy.allhuman.rda
data/deredundancy.allmouse.rda
data/dt_feature_cpp_seed1.fst
data/humantestML.rda
data/mousetestML.rda
data/pepFrag.rda
data/peptides.allclean.rda
data/peptides.allhuman.rda
data/peptides.allmouse.rda
data/peptides.rda
main_running_v3/00_InstallPackage.R
main_running_v3/01_mutate_wholepeptide_single_diffrelation/01_CreatFeatureMatrix_single_diffrelation.R
main_running_v3/01_mutate_wholepeptide_single_diffrelation/02_Model_running.R
main_running_v3/01_mutate_wholepeptide_single_diffrelation/02_Model_running.sbatch
main_running_v3/01_mutate_wholepeptide_single_diffrelation/03_ModelEvaluation_single.R
main_running_v3/02_mutate_wholepeptide_single_samerelation_diffimp/01_CreatFeatureMatrix_single.R
main_running_v3/02_mutate_wholepeptide_single_samerelation_diffimp/02_Model_running.R
main_running_v3/02_mutate_wholepeptide_single_samerelation_diffimp/02_Model_running.sbatch
main_running_v3/02_mutate_wholepeptide_single_samerelation_diffimp/03_ModelEvaluation_single.R
main_running_v3/03_mutate_wholepeptide_double_diffrelation/01_CreatFeatureMatrix_quchong.R
main_running_v3/03_mutate_wholepeptide_double_diffrelation/02_Model_running.R
main_running_v3/03_mutate_wholepeptide_double_diffrelation/02_Model_running.sbatch
main_running_v3/03_mutate_wholepeptide_double_diffrelation/03_ModelEvaluation_single.R
main_running_v3/04_mutate_kmer_single_diffrelation/01_mutateKmerFeature_single.R
main_running_v3/04_mutate_kmer_single_diffrelation/02_Model_running.R
main_running_v3/04_mutate_kmer_single_diffrelation/02_Model_running.sbatch
main_running_v3/04_mutate_kmer_single_diffrelation/03_ModelEvaluation_single.R
main_running_v3/05_mutate_kmer_single_samerelation_diffimp/01_mutateKmerFeature_single.R
main_running_v3/05_mutate_kmer_single_samerelation_diffimp/02_Model_running.R
main_running_v3/05_mutate_kmer_single_samerelation_diffimp/02_Model_running.sbatch
main_running_v3/05_mutate_kmer_single_samerelation_diffimp/03_ModelEvaluation_single.R
main_running_v3/06_mutate_kmer_single_combind_perfect/01_CreatFeatureMatrix_mutate_single.R
main_running_v3/06_mutate_kmer_single_combind_perfect/02_mutateKmerFeature_single.R
main_running_v3/06_mutate_kmer_single_combind_perfect/03_combind.R
main_running_v3/06_mutate_kmer_single_combind_perfect/04_Model_running.R
main_running_v3/06_mutate_kmer_single_combind_perfect/04_Model_running.sbatch
main_running_v3/06_mutate_kmer_single_combind_perfect/05_ModelEvaluation.R
main_running_v3/07_human_kmer_single_diffrelation/02_Model_running.R
main_running_v3/07_human_kmer_single_diffrelation/02_Model_running.sbatch
main_running_v3/07_human_kmer_single_diffrelation/03_Model_evaluation.R
main_running_v3/07_human_kmer_single_diffrelation/HumanKmerFeature_3_8.R
man/BenchmarkEva.Rd
man/CorBetween.Rd
man/CorPlot.Rd
man/FeatureSeByFilter.Rd
man/FeatureSebyAuto.Rd
man/FeatureSebyNestedresam.Rd
man/FeatureSebyVariImpFil.Rd
man/FeatureWrapperMethod.Rd
man/Feature_Calcualtion.Rd
man/Neodataset.Rd
man/PepFeatureDesc.Rd
man/PepFeatureDesc.mutate.Rd
man/PepFrag.Rd
man/PepFragSign.Rd
man/PerformanceEva.Rd
man/Pointbiserial.Rd
man/PropertyofPepSingle.Rd
man/neoML.all.Rd
man/neoML.rpart.Rd
man/pepFragVis.Rd
man/pepVisLength.Rd
man/peptides.Rd
result/.gitkeep
